MD_MAITcellLigands_MDiv_2020

The broadly designed study of molecular dynamics (MD) of receptor complexes of natural MAIT cell ligands, their ethinylated or fluorescence-labelled derivatives generated data that give insights beyond analysis of interactions observed in crystal structures of ternary ligand/MR1/TCR complexes. The data permit a MD weighted appreciation of the crystallographically observed interactions, thereby supporting drug design of MAIT cell ligand. They were notably generated from models of both, binary and ternary complexes of MAIT cell ligands to give insights into the formation of the ternary complexes. Analysis of torsional angles evinces induced-fit of the ligand in binary MR1 complexes upon formation of the corresponding ternary complexes. Radial distribution functions of water around the ethinylated ligands in binary MR1 complexes show that fluorescence labeling by copper(I)-catalyzed azide-alkyne cycloaddition can occur on covalently bound ligand. They also provide a first step to the risk assessment of photon-induced electron transfer (PET) in fluorophore-labelled ligand/MR1 complexes. The dataset contains: * Simulation Interactions Diagram Reports (pdf) and statistics of non-covalent interaction counts (xlsx) of molecular dynamics simulations of natural MAIT cell ligands and their ethinylated or fluorophore-reacted analogs in ternary and binary MR1/TCR and MR1 complexes, respectively. * Raw data of the molecular dynamics simulations: Desmond input and output files as generated by the implementation in Maestro molecular modelling package commercialized by Schrödinger Inc.; compressed; tar archives; The trajectory files found in the directories [MDsimulation_name]_trj have to be decompressed prior to visualization. The 4 simulations of the binary and ternary complexes of 5OERU and 5OPRU are found in archive_natural_ligands_5OERU.tar and archive_natural_ligands_5OPRU.tar. The 4 simulations of the ternary complexes of the R and S stereoisomers of their ethinylated analogues are contained in archive_ethinylated_ligands_SSRR_ternary.tar and archive_ethinylated_ligands_SSRS_ternary.tar while the simulations of the corresponding binary complexes are in archive_ethinylated_ligands_binary.tar. The 4 simulations of the binary complexes of the two stereoisomers of the fluorophore-reacted products are accessible in archive_fluorescent_ligands.tar. Links to other parts of the dataset: https://data.mendeley.com/drafts/txms2vk6jb http://dx.doi.org/10.17632/txms2vk6jb.1 (MD_MAITcellLigands_i_2020) https://data.mendeley.com/drafts/wwxnsj66ks http://dx.doi.org/10.17632/wwxnsj66ks.1 (MD_MAITcellLigands_ii_2020) https://data.mendeley.com/drafts/d9byds5hs6 http://dx.doi.org/10.17632/d9byds5hs6.1 (MD_MAITcellLigands_iii_2020) https://data.mendeley.com/drafts/tp62zb6rg4 http://dx.doi.org/10.17632/tp62zb6rg4.1 (MD_MAITcellLigands_v_2020) https://data.mendeley.com/drafts/4d96x29xkp http://dx.doi.org/10.17632/4d96x29xkp.1 (MD_MAITcellLigands_vi_2020)本研究针对天然黏膜相关恒定T细胞（MAIT）受体复合物的分子动力学（MD）开展了系统性设计，其炔基化或荧光标记衍生物的相关实验数据，为解析三元配体/MR1/TCR复合物晶体结构中观测到的相互作用提供了超越单一晶体结构分析的深入洞察。该数据集可通过分子动力学加权评估晶体学观测到的相互作用，进而助力MAIT细胞配体的药物开发。尤为关键的是，本研究基于MAIT细胞配体的二元及三元复合物模型，为阐明三元复合物的形成机制提供了理论依据。扭转角分析结果表明，二元MR1复合物中的配体在形成对应三元复合物时会发生诱导契合现象。对二元MR1复合物中炔基化配体周围水分子的径向分布函数分析显示，通过铜(I)催化叠氮-炔环加成进行的荧光标记可在共价结合的配体上实现。本数据集同时为荧光团标记配体/MR1复合物中的光诱导电子转移（PET）风险评估迈出了第一步。 本数据集包含以下内容： * 天然MAIT细胞配体及其炔基化或荧光团修饰类似物分别在三元MR1/TCR复合物与二元MR1复合物中的分子动力学模拟的相互作用图解报告（PDF格式）及非共价相互作用计数统计文件（XLSX格式）； * 分子动力学模拟原始数据：由施罗德公司（Schrödinger Inc.）商业化的Maestro分子建模软件包生成的Desmond输入与输出文件，均为压缩tar归档文件； 存储于[MDsimulation_name]_trj目录下的轨迹文件需先完成解压操作后方可进行可视化处理。 其中，5OERU与5OPRU的二元及三元复合物共4组模拟数据存于archive_natural_ligands_5OERU.tar与archive_natural_ligands_5OPRU.tar归档文件中。其炔基化类似物的R和S立体异构体的三元复合物共4组模拟数据包含于archive_ethinylated_ligands_SSRR_ternary.tar与archive_ethinylated_ligands_SSRS_ternary.tar归档文件，对应二元复合物的模拟数据则存于archive_ethinylated_ligands_binary.tar。两种荧光团修饰产物的立体异构体的二元复合物共4组模拟数据可从archive_fluorescent_ligands.tar中获取。 数据集其他部分的链接如下： https://data.mendeley.com/drafts/txms2vk6jb http://dx.doi.org/10.17632/txms2vk6jb.1 (MD_MAITcellLigands_i_2020) https://data.mendeley.com/drafts/wwxnsj66ks http://dx.doi.org/10.17632/wwxnsj66ks.1 (MD_MAITcellLigands_ii_2020) https://data.mendeley.com/drafts/d9byds5hs6 http://dx.doi.org/10.17632/d9byds5hs6.1 (MD_MAITcellLigands_iii_2020) https://data.mendeley.com/drafts/tp62zb6rg4 http://dx.doi.org/10.17632/tp62zb6rg4.1 (MD_MAITcellLigands_v_2020) https://data.mendeley.com/drafts/4d96x29xkp http://dx.doi.org/10.17632/4d96x29xkp.1 (MD_MAITcellLigands_vi_2020)